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ms_xic Class Reference
[Quantitation analysis for Mascot Server and Distiller]

An eXtracted Ion Chromatogram (XIC). More...

#include <ms_xic.hpp>

Inherits matrix_science::ms_handle.

List of all members.

Public Types

enum  peakState {
  PEAK_STATE_UNKNOWN = 0,
  PEAK_STATE_OK = 1,
  PEAK_STATE_DISCARD = 3
}
 

Status codes from fitting peaks.

More...

Public Member Functions

 ms_xic ()
 Default constructor.
 ms_xic (const ms_xic_body &body)
 Populated constructor.
void defaultValues ()
 Use this member to re-initialise internal members.
double getElutionTimeShift () const
 Get the elution time shift in seconds.
unsigned getEndIndex () const
 Get the end index. Only valid if the XIC was processed separately.
int getEndScanId () const
 Get the id of the end scan.
int getNumPoints () const
 Get the number of points.
unsigned getPeakEndIndex () const
 Get the end of the peak. Only valid if the XIC was processed separately.
int getPeakEndScanId () const
 Get the index of the peak end.
unsigned getPeakStartIndex () const
 Get the start of the peak. Only valid if the XIC was processed separately.
int getPeakStartScanId () const
 Get the index of the peak start.
peakState getPeakState () const
 Get the state of the peak.
void getPoint (int index, double &rt, int &scanId, double &intensity) const
 Get a point's values; retention time, scan number and intensity (index 1..n).
unsigned getRegionEndIndex () const
 Get the end of the region. Only valid if the XIC was processed separately.
int getRegionEndScanId () const
 Get the index of the region end.
unsigned getRegionStartIndex () const
 Get the start of the region. Only valid if the XIC was processed separately.
int getRegionStartScanId () const
 Get the index of the region start.
double getRtPeakEnd () const
 Get the retention time of the peak end.
double getRtPeakStart () const
 Get the retention time of the peak start.
double getRtRegionEnd () const
 Get the retention time of the region end.
double getRtRegionStart () const
 Get the retention time of the region start.
unsigned getStartIndex () const
 Get the start index. Only valid if the XIC was processed separately.
int getStartScanId () const
 Get the id of the start scan.
bool getUseTimeShift () const
 Returns true if XIC are aligned based on time instead of scans.
bool hasIndexes () const
 Return true if the functions that return indexes have valid data available to return.

Static Public Member Functions

static peakState getCodeFromXml (std::string text)
 Get the status code for an XML attribute value.
static std::string getXmlCode (peakState code)
 Get the XML attribute value for a status code.

Detailed Description

An eXtracted Ion Chromatogram (XIC).

This consists of a number of individual intensity values.

It also has start and end values and indices for the peaks, regions and the chromatogram itself

This is stored in XML in a "xic" entity.


Member Enumeration Documentation

enum peakState

Status codes from fitting peaks.

See Using enumerated values in Perl, Java, Python and C#.

Enumerator:
PEAK_STATE_UNKNOWN 

initial value

PEAK_STATE_OK 

element is ok

PEAK_STATE_DISCARD 

discard element from calc


Constructor & Destructor Documentation

ms_xic (  )

Default constructor.

Assigns reasonable default values to all internal members.

ms_xic ( const ms_xic_body &  body ) [explicit]

Populated constructor.

Parameters:
bodyThe data loaded from the result file.

Member Function Documentation

void defaultValues (  )

Use this member to re-initialise internal members.

Clears all values

ms_xic::peakState getCodeFromXml ( std::string  text ) [static]

Get the status code for an XML attribute value.

Parameters:
textThe string used to encode the peak state in the XML file.
Returns:
The peak state corresponding to the XML encoded string.
double getElutionTimeShift (  ) const

Get the elution time shift in seconds.

Returns:
The value of the elution time shift.
unsigned getEndIndex (  ) const

Get the end index. Only valid if the XIC was processed separately.

If loaded from XML this may be 0. XML version 1 does not store this information and considerable recalculate would be required to reproduce it.

Returns:
Index at which the the XIC ends.
int getEndScanId (  ) const

Get the id of the end scan.

Returns:
The scan identifier at which the XIC ends.
int getNumPoints (  ) const

Get the number of points.

Returns:
The number of points in the XIC.
unsigned getPeakEndIndex (  ) const

Get the end of the peak. Only valid if the XIC was processed separately.

If loaded from XML this may be 0. XML version 1 does not store this information and considerable recalculate would be required to reproduce it.

Returns:
Index at which the peak ends.
int getPeakEndScanId (  ) const

Get the index of the peak end.

Returns:
The scan identifier at which the peak ends.
unsigned getPeakStartIndex (  ) const

Get the start of the peak. Only valid if the XIC was processed separately.

If loaded from XML this may be 0. XML version 1 does not store this information and considerable recalculate would be required to reproduce it.

Returns:
Index at which the peak starts.
int getPeakStartScanId (  ) const

Get the index of the peak start.

Returns:
The scan identifier at which the peak starts.
ms_xic::peakState getPeakState (  ) const

Get the state of the peak.

Returns:
The peak state.
void getPoint ( int  index,
double &  rt,
int &  scanId,
double &  intensity 
) const

Get a point's values; retention time, scan number and intensity (index 1..n).

Parameters:
indexThe index of the point to be queried (1..number of points).
rtFilled with the retention time of the point.
scanIdFilled with the scan identifier of the point.
intensityFilled with the intensity of the point.
unsigned getRegionEndIndex (  ) const

Get the end of the region. Only valid if the XIC was processed separately.

If loaded from XML this may be 0. XML version 1 does not store this information and considerable recalculate would be required to reproduce it.

Returns:
Index at which the region ends.
int getRegionEndScanId (  ) const

Get the index of the region end.

Returns:
The scan identifier at which the region ends.
unsigned getRegionStartIndex (  ) const

Get the start of the region. Only valid if the XIC was processed separately.

If loaded from XML this may be 0. XML version 1 does not store this information and considerable recalculate would be required to reproduce it.

Returns:
Index at which the region starts.
int getRegionStartScanId (  ) const

Get the index of the region start.

Returns:
The scan identifier at which the region starts.
double getRtPeakEnd (  ) const

Get the retention time of the peak end.

Returns:
The retention time of the peak end.
double getRtPeakStart (  ) const

Get the retention time of the peak start.

Returns:
The retention time of the peak start.
double getRtRegionEnd (  ) const

Get the retention time of the region end.

Returns:
The retention time of the region end.
double getRtRegionStart (  ) const

Get the retention time of the region start.

Returns:
The retention time of the region start.
unsigned getStartIndex (  ) const

Get the start index. Only valid if the XIC was processed separately.

If loaded from XML this may be 0. XML version 1 does not store this information and considerable recalculate would be required to reproduce it.

Returns:
Index at which the the XIC starts.
int getStartScanId (  ) const

Get the id of the start scan.

Returns:
The scan identifier at which the XIC starts.
bool getUseTimeShift (  ) const

Returns true if XIC are aligned based on time instead of scans.

Returns:
True if the elution time shift should be used.
std::string getXmlCode ( ms_xic::peakState  code ) [static]

Get the XML attribute value for a status code.

Parameters:
codeThe peak state to get the XML excoding string for.
Returns:
The string used to encode the peak state in the XML file.
bool hasIndexes (  ) const

Return true if the functions that return indexes have valid data available to return.

XML version 1 does not store this information and considerable recalculate would be required to reproduce it. And it's optional in the XML anyway.

Returns:
True if the XIC has all the index information, otherwise false.

The documentation for this class was generated from the following files:
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:55